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There is a time capsule near the lifts of the Stata Center at the Massachusetts Institute of Technology. It contains items from Building 20, home to fundamental wartime advances in physics, and where, in 1955, a 27-year-old began to transform humanity’s understanding of language. The original ramshackle facility is no more. But the linguist is still here, strolling past in a mustard-coloured puffer jacket.

“Professor Chomsky,” I call out. The 84-year-old greets me and we walk through the new Frank Gehry-designed building, all airy and angular. Students smile and wave and give up more space than Chomsky’s steady gait requires. MIT is in part a monument to his ideas, I suggest. His theories of grammar, which argue that language is innate, have revolutionised modern psychology, computing and cognitive science.

“One of the things about this field is that there’s not a lot you can do with it,” he deadpans, as we pass sleep-deprived coders. (Another example of Chomsky humour: he calls his assistant’s dog, “Cat”.) We step out into the bitter Cambridge day, towards the restaurant. He once came close to joining UC Berkeley, he admits, but California is too hot for him. “I like the cold weather. It means you get work done.”

I tell him I felt the same way when I studied at Harvard. “[Its] faculty doesn’t like me much,” he says. This is not true of the staff of Chomsky’s chosen lunch spot. The Black Sheep welcomes him like the regular he is. A chipper waiter shows us to a table in the corner of the cosy bistro. Perhaps the restaurant’s name is apt, I say. “Not at MIT [but] I don’t have much contact with the main academic world.”

However, Chomsky’s distance from the mainstream is not down to his academic work. Referring to him as a linguist is a bit like calling Arnold Schwarz­enegger a bodybuilder. Chomsky is arguably the world’s most prominent political activist. To his opponents, he is a crank who sees evil as made in America. To his supporters, he is a brave truth-teller and unrelenting huma­nist; a latter-day Bertrand Russell.

I am about to ask the professor about Hugo Chávez, who died the night before our lunch, but a waitress arrives and asks for our order. Chomsky chooses the clam chowder, and a salad with pecans, blue cheese, apples and a lot of adjectives. I go for tomato soup and a salmon salad. The professor asks for a cup of coffee and since we are about to discuss the late Venezuelan leader, I ask for a cup, too.

In 2006, Chávez recommended Chomsky’s Hegemony or Survival: America’s Quest for Global Dominance to the UN General Assembly. “It’s a mixed story,” Chomsky says of Chávez’s legacy. He points to reduced poverty and increased literacy. “On the other hand there are plenty of problems,” such as violence and police corruption; he also mentions western hostility – in particular an attempted coup in 2002 supported by the US. America’s behaviour towards Caracas is obviously important in any assessment of Chávez but its appearance is an early signifier of a pattern in a Chomsky conversation: talk for long enough about politics with the professor and the probability of US foreign policy or National Socialism being mentioned approaches one.

I say that he hasn’t referred to Chávez’s human rights record. Some of Chomsky’s critics have accused him of going easy on the faults of autocrats so long as they are enemies of the US. Chomsky denies this vehemently: he spoke out against the consolidation of power by the state broadcaster; he protested the case of María Lourdes Afiuni, a judge who spent more than a year in prison awaiting trial for releasing a government critic. “And I do a million cases like that one.”

As part of celebrations to mark the FT’s 125th anniversary this year, Penguin is publishing Lunch with the FT: 52 Classic Interviews. The book, served up with glorious colour cartoons, is available as hardback and ebook www.ft.com/lunchbook

Still, Chomsky thinks about how hard to hit his targets. He admits as much as our soups arrive. “Suppose I criticise Iran. What impact does that have? The only impact it has is in fortifying those who want to carry out policies I don’t agree with, like bombing.” He argues that any criticisms about, say, Chávez, will invariably get into the mainstream media, whereas those he makes about the US will go unreported. This unfair treatment is the dissident’s lot, according to Chomsky. Intellectuals like to think of themselves as iconoclasts, he says. “But you take a look through history and it’s the exact opposite. The respected intellectuals are those who conform and serve power interests.”

In 1967 the New York Review of Books published “The Responsibilities of Intellectuals”, a dazzling essay by the then 38-year-old Chomsky. In it he denounced the subservience to power of the Washington intellectual elite. Today he still concentrates his ire on the US on the grounds that it has the most power and he is an American citizen. This makes sense, I say, but doesn’t his position in another community, the anti-war left, mean he also has a duty to call out wrongdoing by its figureheads?

“Maybe some, small percentage should be concerned with that community. But nowhere near the [percentage concerned with the] responsibility for [American] state power and mass media.”

Chomsky has said that, if judged against the principles set out at the Nuremberg Trials, every postwar US leader would be found guilty of war crimes. I ask for his views on Barack Obama. What of the president who opposed the Iraq war? “He’s carrying out a global assassination campaign.” Here is vintage Chomsky, a provocative idea in a matter-of-fact tone, daring the interlocutor to respond. I take the bait, and ask him to explain. “Suppose that some German, Nazi official had been carrying out a global assassination campaign in the west, that would have qualified at Nuremberg.”

Although we are both still slurping soup, the waitress brings us our main courses. This seems like a cue to take a break from war crimes. In an effort to spur reflection I ask whether he feels he has lived up to the standards he set out in his essay in the NYRB all those years ago? “Not really,” he says. “There are a lot of things I should have done more.” He says he began resisting western involvement in Vietnam a decade too late and “that’s only one case”. He wishes he could do more: in eastern Congo, Sri Lanka and on climate change, for instance.

Almost everything, even personal reflections, it seems, comes back to politics. Chomsky has evidently taken to heart Marx’s dictum about the role of the philosopher (“philosophers have only interpreted the world ... The point, however, is to change it”). But does he wish he spent more time doing pure research? “What actually goes is not academia, it’s personal life.” He spends six or seven hours a day answering emails, which leaves little time for hobbies.

“The one thing I’ve found all the way through is to keep time for family.” He has three children, five grandchildren, all of whom are now adults, and a great-grandson who occasionally plays with the restaurant’s toy fire engines. Carol Chomsky, his wife and a fellow linguist, died in 2008. “Since then I’ve dived into work.” I ask whether this was a deliberate, escapist decision. After a rare pause, he says: “Well, John Milton pointed out that the mind is a strange place, so who knows?”

I take the hint and ask about the food. “It’s always good here. I’m not a great gourmet but this is the one place I ever go to.” Like MIT, it is familiar and friendly. “I even get a free drink when I come in the evening.” His tipple is a gin and tonic. Isn’t that an awfully colonial cocktail? “Well, British colonial,” he says, pointing to himself, “I’m a good American.”

Just then, a woman who was seated at the next table comes over, says, “Thank you, so much,” and walks away. Chomsky’s reaction is calm; his bold features don’t flinch under his impressive white mop of hair. “I don’t know who she is,” he says. I tell him he is a celebrity. “It’s a small place.”

The food here is very different from the helpings served by Chomsky’s mother, an immigrant from Belarus, to Noam and his Ukranian-born father, in their home in Philadelphia. Chomsky remembers it fondly, though “by today’s standards, everyone would say it is poison: east European greasy meat, sour cream.”

I ask about his upbringing – did the political drive come before the academic imagination? “Yes, from childhood.” Before he was a teenager he was writing for the school newspaper about the spread of fascism in Europe. “It was pretty scary. My parents would put Hitler’s Nuremberg rally speeches on the radio. I couldn’t understand a word.”

His story reminds me, I say, of the start of Philip Roth’s The Plot Against America, which imagines the repercussions for a Jewish family of a Charles Lindbergh victory in the presidential election of 1940. “It was pretty close to that,” Chomsky says. Which brings me to another criticism of Chomsky, voiced by those such as the late British-born journalist Christopher Hitchens – that opposing the war in Iraq, which began almost exactly 10 years ago, represented the appeasement of a modern-day fascist, Saddam Hussein. “Of course not. If you think he was in the same ballpark as Hitler then you have got to condemn Reagan and Bush number one because they pretty strongly supported him.”

The professor launches into the case for the prosecution. Readers of his book 9/11: Was There an Alternative? will be familiar with his style of argument: to contrast an event perpetrated by an enemy of the US, such as al-Qaeda on September 11, 2001, with an event involving the US, such as the overthrow of President Salvador Allende in Chile on September 11, 1973.

“Just do a simple thought experiment about what we call September 11 ... Imagine that the plane that was downed in Pennsylvania hit its target, which was probably the White House. And suppose it had killed the president, set off a military coup, which had been planned, which overthrew the government, murdered a couple of thousand people, tortured tens of thousands, and established an international terrorist centre that was helping install neo-Nazi governments throughout the region, carrying out assassinations ... It would have been a lot worse than 9/11. Indisputable. And the fact that we can’t see it is a comment on western society and culture.”

The field of comparative massacre makes me feel rather uneasy: the professor’s example implies there is a moral equivalence, I say, between the US and al-Qaeda, and it underplays the responsibility of General Pinochet for the years of oppression that took place after the coup.

“When I compare the two, it isn’t in terms of responsibility, it was in terms of the nature of the atrocity,” he says. “Separate to that comes the question of responsibility. There was no American who sent the planes to kill the [Chilean] president but the US did what it could do to implement the coup.”

We are already running over our scheduled time for lunch. Chomsky has a student waiting, so I skip a few planned questions and ask the one that has been most puzzling in my effort to understand his work. What, if any, is the connection between his academic research and his activism? There seems to be a missing link, I say.

“It has to do with: ‘what is the fundamental core of human nature?’ ” Early Enlightenment thinkers wrote about how it is creative character that separates humans from the rest of the organic world. This character is manifested most clearly in language. Later intellectuals extended this idea to the social sphere. “So, if there is anything that restricts a person’s natural need to carry out creative work under their own direction, that is illegitimate.”

As we get up from the table I ask whether he will always be creatively working. “While I’m upright: there’s a lot to do.”

Does he think about death? “I used to when I was a child. I thought it was terrifying but I got over that stage.”

I explain to Chomsky that the FT picks up the bill. “Brenda Anderson took care of your cheque,” says the waitress. The name isn’t familiar and I suggest to Chomsky that this is probably breaking some kind of rule. “It’s a wonderful place,” he says, unsurprisingly unworried about rule-breaking. He leaves the restaurant before I can find Ms Anderson, who it later turns out is the general manager. “Well, you can go back and give them a big tip. They’re nice people.”

On the way back to the new MIT building, Chomsky points out that his office now looks out on to the Koch building, named after the billionaire brothers and Tea Party supporters. “They’re a lethal force,” he says. What about the Lockheed Martin classroom, I ask, which we pass in the foyer. “I’ve managed to avoid it so far.” He explains that when he joined MIT it was nearly 100 per cent Pentagon-funded “but our lab was also one of the main centres for the anti-war resistance movement”.

We reach the time capsule. What do you think a future historian will write about you, I ask. “I think he’ll have more important topics to write about,” Chomsky says, before warmly greeting the student and apologising for his lateness.

Professor Noam Chomsky will be delivering the 2013 Edward W Said London Lecture, programmed by AM Qattan Foundation/The Mosaic Rooms, on March 18 at 7pm; www.mosaicrooms.org